Stereochemical Criteria for Polypeptide and Protein Chain Conformations

Ramakrishnan, C.; Ramachandran, G.

doi:10.1016/s0006-3495(65)86759-5

Cited by 736 publications

(331 citation statements)

References 15 publications

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“…First, this loop is folded in a compact fashion on the surface of the molecule (Figure 1). All residues have conformations within the favorable regions of the Ramachandran plot (35), in contrast to Ser150 in previous models, which was placed in an unfavorable region. Finally, the average temperature factor for the main-chain atoms within this loop is 36.0 Å 2 (or 38.8 Å 2 for all atoms of residues 144-152), compared with 60 Å 2 , the lowest previously reported (14) (for the structure with PDB code 1asw, also solved with a frozen crystal).…”

Section: Discussioncontrasting

confidence: 59%

Atomic Resolution Structures of the Core Domain of Avian Sarcoma Virus Integrase and Its D64N Mutant^,

et al. 1999

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Six crystal structures of the core domain of integrase (IN) from avian sarcoma virus (ASV) and its active-site derivative containing an Asp64 f Asn substitution have been solved at atomic resolution ranging 1.02-1.42 Å. The high-quality data provide new structural information about the active site of the enzyme and clarify previous inconsistencies in the description of this fragment. The very high resolution of the data and excellent quality of the refined models explain the dynamic properties of IN and the multiple conformations of its disordered residues. They also allow an accurate description of the solvent structure and help to locate other molecules bound to the enzyme. A detailed analysis of the flexible active-site region, in particular the loop formed by residues 144-154, suggests conformational changes which may be associated with substrate binding and enzymatic activity. The pH-dependent conformational changes of the active-site loop correlates with the pH vs activity profile observed for ASV IN.Retroviruses, such as human immunodeficiency virus type 1 (HIV-1) 1 or avian sarcoma virus (ASV), encode in their genes three essential enzymes: reverse transcriptase (RT), protease (PR), and integrase (IN) (1). In rare cases a retrovirus such as feline immunodeficiency virus and equine infectious anemia virus also encodes dUTP-ase (2-4). The first three enzymes are considered to be primary targets for designing drugs against AIDS, because each enzyme is absolutely required for virus replication. Although the search for therapeutically suitable inhibitors has been successful for RT and PR and a number of drugs against these enzymes are already in use (5), no such drugs targeted against IN are yet available. This is due in part to the lack of a complete structural description of IN, which is crucial for understanding its enzymatic activity. Such knowledge is the foundation of rational drug design (6).A molecule of retroviral IN contains approximately 300 amino acids, and it comprises three domains: the zincbinding N-terminal domain, the catalytic core domain, and the DNA-binding C-terminal domain. IN catalyzes the incorporation of reverse-transcribed viral DNA into the host genome in two steps, processing and joining (1,7,8), both of which involve nucleophilic attack by a hydroxyl group on a DNA phosphate. In the processing step, a water molecule attacks near the end of the viral DNA, displacing two nucleotides from the 3′ ends of each of the viral DNA strands. In the joining step, each exposed viral DNA ribose 3′-OH is activated to attack the host DNA at a relatively nonspecific location with a separation of five or six nucleotides, thereby inserting viral DNA into the host genome. In vitro, these reactions require only IN, metal cations, and DNA, although other proteins play a role in vivo.The structures of the N-terminal domain (9, 10) and C-terminal domain (11, 12) of HIV IN have been determined by nuclear magnetic resonance (NMR) spectroscopy, whereas the structure of the catalytic core domain ha...

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Section: Discussioncontrasting

confidence: 59%

Atomic Resolution Structures of the Core Domain of Avian Sarcoma Virus Integrase and Its D64N Mutant^,

et al. 1999

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“…A plot of R factor versus resolution (Luzzati, 1952) is shown in Fig. 2, a Ramachandran plot (Ramakrishnan & Ramachandran, 1965) in Fig. 3 and the distribution of average main-chain and sidechain temperature factors, for the principal conformers, is shown in Fig.…”

Section: Least-squares Refinementmentioning

confidence: 99%

Refinement and structural analysis of bovine cytochrome b5 at 1.5 Å Resolution

Durley¹,

Mathews²

1996

Acta Cryst D

146

198

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The structure of bovine liver cytochrome bs, a soluble 93-residue proteolytic fragment of a 16 kDa. membranebound hemoprotein, initially solved at 2.0A resolution, has been refined at 1.5/~ using data collected on a diffractometer. Refinement to 2.0/~ resolution used the Hendrickson-Konnert procedure PROLSQ and was then extended to 1.5 ~ resolution using the program PROFFT. Only residues 3-87 could be identified in the model and these residues together with 93 water molecules gave an agreement factor of R = 0.161 for data in the resolution range 1.5-5/~,. The structure was finally refined using the program X-PLOR, which enabled alternate conformers to be modelled for several surface side chains. Residues 1 and 2 at the amino terminus of the protein and residue 88 near the carboxyl terminus could be identified from these electron-density maps. However the remaining disordered carboxy-terminal residues could not successfully be included in the model. A total of 117 solvent molecules were included in the final refinement to give R =0.164 for the data between 1.5 and 10/~.

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“…Presumably they are highly disordered. The Ramachandran plot (Ramakrishnan & Ramachandran, 1965), produced by PROCHECK (Laskowski et al, 1993), is shown in Fig. 6.…”

Section: Accuracy Of the Modelmentioning

confidence: 99%

The Refined Structure of dUTPase from Escherichia coli

Dauter¹,

Wilson²,

Larsson³

et al. 1998

Acta Cryst D

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Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase, E.C. 3.6.1.23) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate and is involved in nucleotide metabolism and DNA synthesis. A crystal of the recombinant E. coli enzyme, precipitated from polyethylene glycol mixtures in the presence of succinate at pH 4.2, was used to collect synchrotron diffraction data to 1.9 A resolution, in space group R3, a = b = 86.62, c = 62.23 A. Mercury and platinum derivative data were collected at wavelengths to optimize the anomalous contribution. The resulting 2.2 A MIRAS phases differed from the final set by 40 c on average and produced an excellent map which was easy to interpret. The model contains 132 water molecules and refined to an R value of 13.7%. 136 residues have clear electron density out of 152 expected from the gene sequence. The 16 C-terminal residues are presumably disordered in the crystal lattice. The monomer is a 'jelly-roll' type, containing mostly/3-sheet and only one short helix. The molecule is a tight trimer. A long C-terminal arm extends from one subunit and encompasses the next one within the trimer contributing to its fl-sheet. Conserved sequence motifs common among dUTPases, previously suggested to compose the active site and confirmed in a recent study of the dUDP complex, are located at subunit-subunit interfaces along the threefold axis, in parts of the fl-sheet and in loop regions. A similar molecular architecture has recently been found in two other trimeric dUTPases.

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Stereochemical Criteria for Polypeptide and Protein Chain Conformations

Cited by 736 publications

References 15 publications

Atomic Resolution Structures of the Core Domain of Avian Sarcoma Virus Integrase and Its D64N Mutant^,

Atomic Resolution Structures of the Core Domain of Avian Sarcoma Virus Integrase and Its D64N Mutant^,

Refinement and structural analysis of bovine cytochrome b5 at 1.5 Å Resolution

The Refined Structure of dUTPase from Escherichia coli

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Stereochemical Criteria for Polypeptide and Protein Chain Conformations

Cited by 736 publications

References 15 publications

Atomic Resolution Structures of the Core Domain of Avian Sarcoma Virus Integrase and Its D64N Mutant,

Atomic Resolution Structures of the Core Domain of Avian Sarcoma Virus Integrase and Its D64N Mutant,

Refinement and structural analysis of bovine cytochrome b5 at 1.5 Å Resolution

The Refined Structure of dUTPase from Escherichia coli

Contact Info

Product

Resources

About

Atomic Resolution Structures of the Core Domain of Avian Sarcoma Virus Integrase and Its D64N Mutant^,

Atomic Resolution Structures of the Core Domain of Avian Sarcoma Virus Integrase and Its D64N Mutant^,